[petsc-users] Is MatSetUp required with MatCreateNormal and MatCreateMPIAIJWithSplitArrays?

[Barry Smith]

   Mihai,

    Thanks for tracking down the problem. As a side note, you are getting close to using all of the space in int in your matrix row/column sizes, when you matrix sizes are great than 2^{31}-1 you will need to configure PETSc with --with-64-bit-indices to have PETSc use long long int for PetscInt.

   Satish,

     Could you please patch 3.3 and replace the use of %D with %lld and replace the (PetscInt) casts with (long long int) casts in the two lines
      ierr = PetscViewerASCIIPrintf(viewer,"total: nonzeros=%D, allocated nonzeros=%D\n",(PetscInt)info.nz_used,(PetscInt)info.nz_allocated);CHKERRQ(ierr);
        ierr = PetscViewerASCIIPrintf(viewer,"total number of mallocs used during MatSetValues calls =%D\n",(PetscInt)info.mallocs);CHKERRQ(ierr);

  Thanks

   Barry

On Dec 14, 2012, at 4:59 AM, Mihai Alexe <malexe at vt.edu> wrote:

> Barry,
> 
> I've tracked down the problem.
> 
> I ran with -info -mat_view_info, and fpe's enabled and got a SIGFPE after entering MatCreateMPIAIJWithSplitArrays (Petsc did not produce a stacktrace unfortunately). This was due to a floating point exception in a typecast inside mat/interface/matrix.c:
> 
>       if (mat->ops->getinfo) {
>         MatInfo info;
>         ierr = MatGetInfo(mat,MAT_GLOBAL_SUM,&info);CHKERRQ(ierr);
>         ierr = PetscViewerASCIIPrintf(viewer,"total: nonzeros=%D, allocated nonzeros=%D\n",(PetscInt)info.nz_used,(PetscInt)info.nz_allocated);CHKERRQ(ierr);
>         ierr = PetscViewerASCIIPrintf(viewer,"total number of mallocs used during MatSetValues calls =%D\n",(PetscInt)info.mallocs);CHKERRQ(ierr);
>       }
> 
> My sparse matrix has about 6 billion nonzeros. When I disable FPEs, i get a silent overflow when converting MatInfo.nz_used from PetscLogDouble to (32-bit) PetscInt:
> 
> Matrix Object: 96 MPI processes
>   type: mpiaij
>   rows=131857963, cols=18752388
>   total: nonzeros=-2147483648, allocated nonzeros=0 
> 
> and the code runs just fine. Maybe PETSc should cast nz_used to a long int?
> 
> 
> Mihai
> On Thu, Nov 29, 2012 at 6:25 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> 
> On Nov 29, 2012, at 9:48 AM, Mihai Alexe <malexe at vt.edu> wrote:
> 
> > Hello all,
> >
> > I am creating a large rectangular MPIAIJ matrix, then a shell NormalMatrix that eventually gets passed to a KSP object (all part of a constrained least-squares solver).
> > Code looks as follows:
> >
> >  //user.A_mat and user.Hess are PETSc Mat
> >
> >  info = MatCreateMPIAIJWithSplitArrays( PETSC_COMM_WORLD, *locrow, *loccol, nrow,
> >                                 *ncol, onrowidx, oncolidx,
> >                                 (PetscScalar*) onvals, offrowidx, offcolidx,
> >                                 (PetscScalar*) values, &user.A_mat ); CHKERRQ(info);
> >
> >  info = MatCreateNormal( user.A_mat, &user.Hess ); CHKERRQ(info);
> >  info = MatSetUp( user.Hess );
> >
> > Is MatSetUp() required for A or Hess to be initialized correctly? Or some call to MatSetPreallocation?
> '
>    No you shouldn't need them.   Try with valgrind   http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> 
>   Barry
> 
> >
> > My code crashes after displaying (with -info -mat_view_info):
> >
> > [0] PetscCommDuplicate(): Duplicating a communicator 47534399113024 67425648 max tags = 2147483647
> > [0] PetscCommDuplicate(): Duplicating a communicator 47534399112000 67760592 max tags = 2147483647
> > [0] MatCreate_SeqAIJ_Inode(): Not using Inode routines due to -mat_no_inode
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615
> > Matrix Object: 1 MPI processes
> >   type: seqaij
> >   rows=8920860, cols=1508490
> >   total: nonzeros=34572269, allocated nonzeros=0
> >   total number of mallocs used during MatSetValues calls =0
> >     not using I-node routines
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592
> > [0] MatCreate_SeqAIJ_Inode(): Not using Inode routines due to -mat_no_inode
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 18752388; storage space: 0 unneeded,1762711 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349
> > Matrix Object: 1 MPI processes
> >   type: seqaij
> >   rows=8920860, cols=18752388
> >   total: nonzeros=1762711, allocated nonzeros=0
> >   total number of mallocs used during MatSetValues calls =0
> >     not using I-node routines
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615
> > Matrix Object: 1 MPI processes
> >   type: seqaij
> >   rows=8920860, cols=1508490
> >   total: nonzeros=34572269, allocated nonzeros=0
> >   total number of mallocs used during MatSetValues calls =0
> >     not using I-node routines
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 18752388; storage space: 0 unneeded,1762711 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349
> > Matrix Object: 1 MPI processes
> >   type: seqaij
> >   rows=8920860, cols=18752388
> >   total: nonzeros=1762711, allocated nonzeros=0
> >   total number of mallocs used during MatSetValues calls =0
> >     not using I-node routines
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 1508490; storage space: 0 unneeded,34572269 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 615
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592
> > [0] PetscCommDuplicate(): Using internal PETSc communicator 47534399112000 67760592
> > [0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
> > [0] VecScatterCreate(): General case: MPI to Seq
> > [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 8920860 X 38109; storage space: 0 unneeded,1762711 used
> > [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> > [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 349
> > Matrix Object: 160 MPI processes
> >   type: mpiaij
> >   rows=131858910, cols=18752388
> >
> > The code ran just fine on a smaller (pruned) input dataset.
> > I don't get a stacktrace unfortunately... (running in production mode, trying to switch to debug mode now).
> >
> >
> > Regards,
> > Mihai
> >
> 
>